AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i179_folate_biosynthesis_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #2 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #3 dedA 82 orf, hypothetical protein #4 usg 65 putative PTS system enzyme II A component #5 pdxB 98 erythronate-4-phosphate dehyrogenase #6 holC 52 DNA polymerase III, chi subunit #7 BIME233 22 BIME #8 pepA 266 aminopeptidase A/I #9 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) #10 HI1394 221 conserved hypothetical protein #11 HI1396 84 H. influenzae predicted coding region HI1396 #12 HI1397 234 DNA polymerase III, chi subunit (holC) Motif number 1 TGTTGGGGGCAAAAATGGCATTATGCGTCCCCA 2 88 1 AAAAAGATTA 0.882109 -68 TTAAGCCATGAAACAAGCTAAAATCCTGCAAAA 8 37 0 AAACAGAAAA 0.897839 -230 AAATACTCCAAAATAAATTTCAG 9 1 1 AAATATAAAA 0.603409 -193 CTGTAAGACAAAAAAATAAAAAAAATGTTCAAT 9 44 1 AAAAATAAAA 0.929258 -150 GGAGCAGTACAAAAACGGTCTTACAAGTAGCAA 9 113 1 AAAAAGCTTA 0.790677 -81 TCTAGTCAATAAAAAGGTCAAAAA 9 180 1 AAAAAGAAAA 0.965299 -14 CAATATGACAAAACAAGAAATAAATTATCTAAA 10 16 0 AAACAGATAA 0.920471 -206 TATCATAAATAAAAATTTCATCACAATATGACA 10 39 0 AAAAATATCA 0.748097 -183 CCAGCTTGGTAAAAATTCACTAAATTGAGTAAT 10 119 0 AAAAATCTAA 0.897258 -103 AAGCTGGTGTAAAAAAGTATTAAATCAATTGAT 10 145 1 AAAAAGTTAA 0.823161 -77 TAGGATTTGTAAAAACTTTCTAAAACCTAACCG 10 183 1 AAAAATCTAA 0.897258 -39 GGAACGTAACAAAAACGTTAAAAATCAGTTTTG 12 77 1 AAAAAGAAAA 0.965299 -158 AAAAAACCCTAAAAAATAAATAATTAAATATGC 12 158 0 AAAAATATAA 0.945353 -77 CTTACCCTATAAAAAGGGTAAAATTTTAACGAA 12 189 0 AAAAAGAAAA 0.965299 -46 ***** * **** Masking position 5 Map Score: 14.038 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 258 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 2 AAAGTTTCGGGCTGTTATGTTTTAATGTGCAACAT 2 45 1 GCGTATTTAA 0.982162 -111 TGTAGCCACCGCCGTTGTCTTTAAGATTCAGGAGC 8 235 1 GCGTGTTTAG 0.995914 -32 ATTGAGTAATGCAGTTATCTTTTAGTTGAAAAATC 10 94 0 GCGTATTTAG 0.99507 -128 TCCTTAAAGAGCGGTTAGGTTTTAGAAAGTTTTTA 10 192 0 GCGTATTTAG 0.99507 -30 TTTTATCAACGCTTTCAATTTTGAGTATTGAGCAG 11 29 1 GCTTATTTAG 0.963208 -56 TGAGTATTGAGCAGTAGGTTTTGAATTAATTAAAG 11 50 1 GCGTGTTTAA 0.985183 -35 TCATAAAAGCGCGGTGGATTTTCAGACATTTGTAA 12 119 1 GCGTGTTTAG 0.995914 -116 ** ** * *** ** Masking position 14 Map Score: 12.8368 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 24 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 GCAGAGCCAGTGGCCCTGCCCTTATCAGTTA 1 9 0 TGGCCGCCTT 0.974446 -61 GCAGGGCCACTGGCTCTGCCCTTTTGCTATTCT 1 23 1 TGGCTGCCTT 0.962587 -47 TTCAGGCTGTAGCCAACGTAGTTACAGCCTGAA 3 32 1 AGCCAGTGTT 0.894532 -51 GCTGTAACATTGGCAGGGAGCTTTGCTATTTCT 4 30 1 TGGCAGACTT 0.941284 -36 TTGCGTCAGGCAAGGCTGTTAT 7 8 1 AGGCAGCGTT 0.989483 -15 TGTTCTGACGTGCCAATGCCGTAATAACGTTAA 8 144 1 TGCCAGCGTA 0.936514 -123 TTCTATCTGTAGCCACCGCCGTTGTCTTTAAGA 8 228 1 AGCCAGCGTT 0.987 -39 ATGATAACTCTGGCATTGCGCTTGAATTGATTT 10 66 1 TGGCAGCCTT 0.993082 -156 ATGTCTGAAAATCCACCGCGCTTTTATGATCTA 12 115 0 ATCCAGCCTT 0.901873 -120 ***** ** *** Masking position 12 Map Score: 9.05478 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 318 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 TATCCAAAGTTTCGGGCTGTTATGTTTTAA 2 40 1 TTCGGGCTGT 0.986873 -116 ATGTGCAACATTCATGGTCTGTTGGGGGCA 2 69 1 TTCATGGTCT 0.935239 -87 CTCGGAACATTTCAGGCTGTAGCCAACGTA 3 22 1 TTCAGGCTGT 0.994043 -61 CTCGTCATCTTTCAGGCTGTAACTACGTTG 3 45 0 TTCAGGCTGT 0.994043 -38 TCTCTTCTTCATGCTCTCTGCTGTAAC 4 8 1 TTCATGCTCT 0.980713 -58 ********** Masking position 8 Map Score: 5.39482 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 75 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GCAGAGCCAGTGGCCCTGCCCTTATCAGTT 1 12 0 TGGCCCTGCC 0.988939 -58 GCAGGGCCACTGGCTCTGCCCTTTTGCTAT 1 23 1 TGGCTCTGCC 0.988068 -47 ATTTGCCTATGCCTTGTACTCGT 3 70 0 TGCCTATGCC 0.96385 -13 TCTTCTTCATGCTCTCTGCTGTAACATTGG 4 13 1 GCTCTCTGCT 0.814258 -53 AAATAGCAAAGCTCCCTGCCAATGTTACAG 4 31 0 GCTCCCTGCC 0.973322 -35 TGTTCTGACGTGCCAATGCCGTAATAACGT 8 144 1 TGCCAATGCC 0.950427 -123 ATCAATTCAAGCGCAATGCCAGAGTTATCA 10 67 0 GCGCAATGCC 0.962588 -155 ********** Masking position 7 Map Score: 4.03936 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 601 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 AGGCATACTTGCGAAGATTTCAGGTATAAGG 5 18 0 GCGAAGATTC 0.928239 -81 GCTGCGGTGTATACCTGATGCGTA 6 4 1 GCGGTGTTAC 0.949095 -49 GGGGCTTCTTGTGGTGGATTTAAATACGCAT 6 28 0 GTGGTGGTTT 0.857655 -25 AATTATCTTAGCGACGATTTCGACGACTCAA 8 85 0 GCGACGATTC 0.950421 -182 GTCCGCTGTTGCGATGACTTCGTGTTAATCT 8 176 0 GCGATGATTC 0.981279 -91 AAAGACAACGGCGGTGGCTACAGATAGAATT 8 226 0 GCGGTGGTAC 0.986671 -41 TCATAAAAGCGCGGTGGATTTTCAGACATTT 12 119 1 GCGGTGGTTT 0.978926 -116 ******* *** Masking position 9 Map Score: 3.84881 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 627 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 CGTTATCTGAAATTTATTTTGGAGTATTT 9 10 0 AATTTATTTT 0.952064 -184 AAATTCTATAAATTTATGTTCTAATACGCG 9 144 1 AATTTATGTT 0.8405 -50 AAGTTTAGATAATTTATTTCTTGTTTTGTC 10 13 1 AATTTATTTC 0.85952 -209 ATTGCGCTTGAATTGATTTTTCAACTAAAA 10 80 1 AATTGATTTT 0.969267 -142 TAGATTTATCAATTGATTTAATACTTTTTT 10 155 0 AATTGATTTA 0.867515 -67 ATTAAAACGCAAGTGATTTTAACACTTCCG 12 37 1 AAGTGATTTT 0.906584 -198 TATGTCACAAAACTGATTTTTAACGTTTTT 12 87 0 AACTGATTTT 0.906573 -148 CATATTTAATTATTTATTTTTTAGGGTTTT 12 159 1 TATTTATTTT 0.780861 -76 ********** Masking position 6 Map Score: 4.58828 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 77 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 GCTGTTATGTTTTAATGTGCAACATTCATG 2 55 1 TTTAATGTGC 0.892785 -101 TGTGGTGGATTTAAATACGCATCAGGTATA 6 20 0 TTAAATACGC 0.983519 -33 TTTAAATACGCCCGTAAAAAC 8 2 1 TTAAATACGC 0.983519 -265 AAATTTATGTTCTAATACGCGCAATTTTCT 9 153 1 TCTAATACGC 0.949397 -41 AAATAAATAATTAAATATGCATTATTACAA 12 148 0 TTAAATATGC 0.963615 -87 ********** Masking position 5 Map Score: 2.88937 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 49 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 CGTCCCCAAAGATAAAACTGGCATCGAACCA 2 113 1 GATAAAACTG 0.968279 -43 CACTTGTCCGGTTAACTCTCGTCTCATACAG 5 67 1 GTTAACTCTG 0.970546 -32 AAATACGCCCGTAAAAACTCGTCTTTTGCAG 8 14 1 GTAAAAACTG 0.866218 -253 TTTTATTTATGATAACTCTGGCATTGCGCTT 10 58 1 GATAACTCTG 0.97926 -164 TAAATCAATTGATAAATCTAGGATTTGTAAA 10 165 1 GATAAATCTG 0.977648 -57 ********* * Masking position 5 Map Score: 1.11493 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 36 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CTGATTCGTTACGGTGAGAATAGCAAAAGGGCAGAG 1 36 0 AGAGAAGCAA 0.977719 -34 TACAGCCTGAAAGATGACGAGTACAAGGCATAGGCA 3 54 1 AGACATACAA 0.903744 -29 GGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAA 8 212 0 ATAGATGCAA 0.964932 -55 AAAAATGTTCAATAAGAGGAGAGCAAATTATCTTGT 9 64 1 AGAGAAGCAA 0.977719 -130 TTTAAAAGGAAATCGGAGCAGTACAAAAACGGTCTT 9 99 1 AGAGATACAA 0.979935 -95 AAAATTCACTAAATTGAGTAATGCAGTTATCTTTTA 10 105 0 AGAGATGCAG 0.985481 -117 TTTTCATTCAATTCATAGGAGTACAGA 12 2 0 ATAGATACAG 0.89965 -233 * *** * ***** Masking position 7 Map Score: 1.391 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 75 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 CCGTTGAGTATAATTATCTTAGCGACGATT 8 97 0 TAATTATCTT 0.910608 -170 AGAGGAGAGCAAATTATCTTGTTTAAAAGG 9 78 1 AAATTATCTT 0.946949 -116 CTAATACGCGCAATTTTCTAGTCAATAAAA 9 164 1 CAATTTTCTA 0.842943 -30 AACAAGAAATAAATTATCTAAACTTAT 10 8 0 AAATTATCTA 0.905902 -214 TTGAGTAATGCAGTTATCTTTTAGTTGAAA 10 98 0 CAGTTATCTT 0.935808 -124 CAATTATCCTCTTTAATTAA 11 75 0 CAATTATCCT 0.936875 -10 ********** Masking position 5 Map Score: 0.467243 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 72 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 ********** No masking Map Score: 2.27617e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: 2.27617e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 2.27617e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0